Looking for a diploma topic in (micro)biology?
If you're a (micro)biology student interested in environmental aspects but with a good deal of molecular biology, we might be able to offer you a few exciting topics. If you are interested, please come and discuss with us. Contact: Jan Roelof van der Meer.
Evolution of Catabolic Pathways
ICEclc is a conjugative DNA element that is normally integrated in the chromosome of its host bacterium Pseudomonas knackmussii. Transfer is only initiated in a few percent of cells during stationary phase, which we have called 'transfer competent' cells. The formation of transfer competence is thought to be the consequence of a 'bistable' decision (i.e., cells in a population follow two different processes: active transfer or no transfer at all). Cells that follow the transfer process express several promoters on ICEclc simultaneously, whereas those promoters are silent in other cells. Interestingly, these promoters are also silent in other Pseudomonas species that do not have ICEclc. The main goal of the project is to better understand how bistability is generated and, in particular, to find possible sequence features in bistable promoters that may determine bistability.
Applied microbial ecology
1) Task division in the oil-degrading bacterium Alcanivorax borkumensis
Bacterial species are traditionally perceived as 'clonal' and, therefore, all cells within a clonal population are supposed to be performing, with a certain degree of variability, the same metabolic tasks. More recently the concept of phenotypic identity has been challenged by the discovery of bistable programs, such as sporulation, DNA uptake or ICE conjugation. Furthermore, there is increasing evidence for 'task division', by which phenotypically different cells in a clonal population diverge in tasks they perform for the population as a whole. The goal of this master project is to study whether task division occurs among cells in a population of the oil-degrading bacterium Alcanivorax borkumensis.
2) Microbial biogeography in the Western Swiss Alps
The wide elevation gradients and topographic heterogeneity in the Alps presents a unique opportunity to study the biogeography of soil microorganisms in relation to plant diversity as well as climatic and physicochemical factors. The masters project will contribute to a larger collaborative project between the DEE and the DMF whose goal is to understand alpine microbial biodiversity and biogeography from an ecological habitat perspective. The main goal of this masters project is to study microdiversity of microorganisms involved in the nitrogen cycle within microbial communities in alpine soil across a very wide elevational gradient.
Development of whole-cell biosensors
1) Functional analysis of ribose binding protein, a potential target protein for bioinformatic predictions of new substrate binding properties
Ribose binding protein (RBP) is a periplasmic binding protein that bacteria such as Escherichia coli use to detect ribose by chemotaxis. RBP can be used in artificial signaling chains to produce so-called 'biosensor' bacteria that detect chemicals and produce light. The potential advantage of using RBP is that its crystal structure is known and that predictions can be made by molecular dynamic models on which amino acids to change to obtain new target specificities. Yet, despite several (published and unpublished) attempts to engineer the protein to bind other target molecules than ribose, the predictions have a poor success rate. The reason for this might be that it is insufficiently understood which amino acids of RBP have critical roles in processes other than ribose binding (for example, binding to a receptor or protein folding).
In this project we would like to use a technique called alanine-scanning to test the effect of functional replacement of every individual amino acid of RBP by alanine.
2) Toggle gene circuits as tunable digital responders to monitor arsenic water contamination.
Contamination with arsenic is a recurring problem in both industrialized and developing countries. Of particular concern is the contamination of potable water sources by arsenic in Southeast Asia (Bangladesh, Vietnam). In order to provide alternative measurement tools for detection arsenic contamination, our group has developed a number of bioassays with so-called reporter bacteria. These bacteria respond to the presence of arsenic by synthesizing an easily measurable reporter protein, which can be accurately quantified from calibration curves.
Despite the sensitivity of current arsenic bioreporters it would be more simple for 'field applications' to have a sensor characterized by a threshold response, below which no signal and above which a maximal signal is produced. An array of this type of biosensors each with an increasing threshold would allow easy quantification of arsenic concentrations by direct observation of yes/no signals in individual biosensor spots. The aim of the project is to try and produce a set of digitally responding arsenic biosensors by using toggle switches.